Jérôme Hert wrote:
> Dear Colleaugues,
>
> I was trying to use an option when converting a file into a different
> format.
>
> I use Perl so I write something like
> use Chemistry::OpenBabel;
> my $obMol = new Chemistry::OpenBabel::OBMol;
> my $obConversion = new Chemistry::OpenBabel::OBConversion;
> $obConversion->SetInAndOutFormats( "mol2", "pdb" );
> $obConversion->ReadFile( $obMol, "infile.mol2");
> $obConversion->WriteFile( $obMol, "outfile.pdb" );
>
> That works fine.
>
> Now I am trying to add something like:
> $obConversion->AddOption("d");
> before reading thr file in, the program doesn't complain but nothing
> happens (i.e., the hydrogens are still present in the output file).
>
> Anybody has any idea how these options are named? Any has any clue about
> all those GetOptions, SetOption, GetOptions etc of that class in Perl?
>
In C++ it would be necessary to use:
obConversion->AddOption("d", OBConversion::GENOPTIONS);
where the second parameter is an enum. I don't know how this is
translated with the scripting interfaces.
There are three types of option INOPTIONS, OUTOPTIONS and GENOPTIONS.
On the babel command-line the INOPTIONS, OUTOPTIONS have a prefix,
e.g. -as and -xn respectively.
The default for this function is OUTOPTIONS, but -d needs GENOPTIONS.
Multi-character options are all GENOPTIONS.
It's a bit confusing for the scripting interface user, and perhaps we
need something like AddGenOption("d")
You could also use a direct function call of DeleteHydrogens().
Chris
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